Blender render recalculate faces on shape key animation
There is probably a problem with the shape key animation: Since you are using quad faces, you have to deal with the fact that two edges of that face can make an angle of more than 180 degrees. This is not correct.

Correct:



Here you can see that there is a triangle formed between those three vertices. They actually have a part of the face to close.

Incorrect (your case):


Here, the angle is over 180 degrees. Blender still wants those three vertices to hold up that face. It gets confused. It wants to keep that straight line between the two vertices, but it will happen outside of the preferred boundaries. It's just like folding over a piece of paper like this, and pressing them so much together, that they interfere with each other. In some situations, it will result in a very strange defect in your geometry.

So, technically speaking: your shape key animation is the source of the problem. The vertices move to far into their own faces.